NOTE: This was a huge wall of text, I've tried to cut it down as much as possible, but I'm trying to tell the whole story so I'm not accused of failing to do so 
I homebrewed my Wii U last week according to P3nce's youtube video tutorial - it worked like a charm.
(for the record i've shown my syscheck file to support helpers elsewhere and my installation is fine)
First off, without any Wii U games to rip and store, I put my gamecube and Wii archives onto an external 500GB SSD hard drive and played them with USB Loader GX on the vWii with near total success.
Once some ordered titles started arriving, I began looking into options for getting Wii U games going. I decided that it was a waste to put 70GB or so of GCN/Wii games on that 500GB SSD, so I took that SSD, cleared out all the folders on it, and let the Wii U format it to be an install USB for the 180-odd GB of Wii U games I would transfer across with my SD card.
So far so good, I am now able to play Wii U games - with some exceptions - without much trouble.*
*I think I got the update/DLC installation a bit wrong on a few of the titles, whatever, some of them don't seem to run, Xenoblade seems to freeze my system, but Breath of the Wild works, among others
In the mean time, I put a few GBA roms on my SD card and played them in my vWii using visualboy advance via the USB Loader GX menu.
THE PROBLEM IS HAPPENING NOW, because a 128GB USB drive arrived from Amazon and I wanted to put my gamecube and wii archives onto it.
The USB crapped out and just failed on me.
So, reluctantly, I tried to use a new hard drive that I had intended to use for my PS4 Pro extended storage - a 2 TB WD_Black HDD - for Wii/GCN games. So yeah all-in-all I've traded in a 500GB SSD for a 2TB HDD for my 70-odd GB of Wii and GCN images. Bit of a cluster fuck, really...
This is where stuff went wrong.
On my laptop I have a sort of backup of the folders from my 500GB SSD when my Wii/GCN games were working at the start. They're all there in their folders, formatted just like they should be by 'Wii Backup Manager", copy/pasted from the Drive. I took these backups and simply copy/pasted them across onto my 2TB WD_Black HDD.
Then, with a Y-Cable to power the drive, I turned off my Wii U, connected the data USB into the top of the two rear USB ports, and the power USB into the bottom port.
I turned on the Wii U, navigated to vWii, opened USB Loader GX... and the only files I can see in the 'games' list are all the emulators on my SD card.
I don't see any GCN or Wii games, like I did before when I had just jailbroken the thing according to P3nce's tutorial.
I think to myself: "Okay, I tried to play those GBA games, so I've got my USB Loader GX looking at my SD for roms, not my USB. So I go into settings > Hard Drives > and switched my drive from 'SD' to 'FAT32 1890 GB', or whatever it's called. Should work now, right? wrong.
I restart USB Loader GX. I restart my console. I open USB Loader GX from INSIDE USB Loader GX (this time it says 'waiting for HDD' and counts down from 20, or something, but apparently my HDD fails to communicate). It doesn't show my game files. I even tried plugging my HDD into the Wii U and the power lead from the Y-cable into my laptop to make sure it was getting enough power.
Nintendont isn't on my vWii menu for some reason, but I opened it via USB Loader GX and I was able to SEE AND PLAY my gamecube games - but they all said "There is no memory card in slot A" and I couldn't save. I went to try fiddle with the Nintendont settings and 'mount' a memory card, but I couldn't find it again and I rage quit and came here for help.
I homebrewed my Wii U last week according to P3nce's youtube video tutorial - it worked like a charm.
(for the record i've shown my syscheck file to support helpers elsewhere and my installation is fine)
First off, without any Wii U games to rip and store, I put my gamecube and Wii archives onto an external 500GB SSD hard drive and played them with USB Loader GX on the vWii with near total success.
Once some ordered titles started arriving, I began looking into options for getting Wii U games going. I decided that it was a waste to put 70GB or so of GCN/Wii games on that 500GB SSD, so I took that SSD, cleared out all the folders on it, and let the Wii U format it to be an install USB for the 180-odd GB of Wii U games I would transfer across with my SD card.
So far so good, I am now able to play Wii U games - with some exceptions - without much trouble.*
*I think I got the update/DLC installation a bit wrong on a few of the titles, whatever, some of them don't seem to run, Xenoblade seems to freeze my system, but Breath of the Wild works, among others
In the mean time, I put a few GBA roms on my SD card and played them in my vWii using visualboy advance via the USB Loader GX menu.
THE PROBLEM IS HAPPENING NOW, because a 128GB USB drive arrived from Amazon and I wanted to put my gamecube and wii archives onto it.
The USB crapped out and just failed on me.
So, reluctantly, I tried to use a new hard drive that I had intended to use for my PS4 Pro extended storage - a 2 TB WD_Black HDD - for Wii/GCN games. So yeah all-in-all I've traded in a 500GB SSD for a 2TB HDD for my 70-odd GB of Wii and GCN images. Bit of a cluster fuck, really...
This is where stuff went wrong.
On my laptop I have a sort of backup of the folders from my 500GB SSD when my Wii/GCN games were working at the start. They're all there in their folders, formatted just like they should be by 'Wii Backup Manager", copy/pasted from the Drive. I took these backups and simply copy/pasted them across onto my 2TB WD_Black HDD.
Then, with a Y-Cable to power the drive, I turned off my Wii U, connected the data USB into the top of the two rear USB ports, and the power USB into the bottom port.
I turned on the Wii U, navigated to vWii, opened USB Loader GX... and the only files I can see in the 'games' list are all the emulators on my SD card.
I don't see any GCN or Wii games, like I did before when I had just jailbroken the thing according to P3nce's tutorial.
I think to myself: "Okay, I tried to play those GBA games, so I've got my USB Loader GX looking at my SD for roms, not my USB. So I go into settings > Hard Drives > and switched my drive from 'SD' to 'FAT32 1890 GB', or whatever it's called. Should work now, right? wrong.
I restart USB Loader GX. I restart my console. I open USB Loader GX from INSIDE USB Loader GX (this time it says 'waiting for HDD' and counts down from 20, or something, but apparently my HDD fails to communicate). It doesn't show my game files. I even tried plugging my HDD into the Wii U and the power lead from the Y-cable into my laptop to make sure it was getting enough power.
Nintendont isn't on my vWii menu for some reason, but I opened it via USB Loader GX and I was able to SEE AND PLAY my gamecube games - but they all said "There is no memory card in slot A" and I couldn't save. I went to try fiddle with the Nintendont settings and 'mount' a memory card, but I couldn't find it again and I rage quit and came here for help.
So, in summary, I stand here:
Condition A: (until a few days ago) Recently jailbroken, everything works well, don't have any Wii U games but Wii and GCN games are all emulating more or less perfectly from a WD 500GB SSD external drive.
Condition B: Decided to back track, removed Wii/GCN games from that 500GB SSD drive and used it to install Wii U games instead. Wii U games for the most part work fine. I also use my SD card to play some GBA roms via vWii using VisualBoy Advance.
Condition C: (current condition) Try to use a second external hard drive (WD_BLACK 2TB HDD) for storing the Wii and GCN games that worked fine previously, but USB Loader GX on my vWii doesn't read my HDD and the 'game' list in USB L GX is populated by the emulators on my SD card. I can't make it read my new hard drive, the obvious option where I change the hard drive from "SD" to "FAT32 1920 GB", or whatever it's called, doesn't make a difference. I can SEE AND PLAY the games via nintendont, which I open through USB Loader gx, but it doesn't have a memory card mounted. I'd rather have it work like it used t.
Huge appreciation to anyone who can read that/help me out. Really want to get this working correctly.
